Germanium is a semiconductor that offers great promise in certain semiconductor devices and structures, most notably for channel materials in advanced metal-oxide-semiconductor field-effect transistors (MOSFETs). When growing germanium on silicon in heteroepitaxial processes, germanium may be selectively grown in trenches of a patterned silicon substrate. Any imperfections in the crystalline germanium, as deposited, may be removed by annealing, which is typically done by a thermal process. In a conventional process, the substrate is heated to an anneal temperature to drive any imperfections or dislocations to the interface between the silicon and the germanium. However, in conventional processes, the thermal treatment frequently results in extrusion of the germanium from the trenches. Therefore, there is a need for an improved process for thermal treatment of silicon-germanium heteroepitaxial structures.